source("helper_functions.R")
library(cytokit)
library(ggedit)
library(kableExtra)
library(monocle)
library(patchwork)
library(readxl)
library(readr)
library(R.utils)
library(Seurat)
library(tidyverse)
library(viridis)
sample <- c("joint_pons.seurat")
tables_directory <- "tables"
dir.create(tables_directory, showWarnings = FALSE)
monocle_objects_directory <- "monocle_objects"
dir.create(monocle_objects_directory, showWarnings = FALSE)
input_directory <- "/mnt/KLEINMAN_SCRATCH/projects/sjessa/from_hydra/single_cell/2019-02_revision1/output/atlas-02"
load(file.path(input_directory, "joint_pons.seurat.Rda"))
seurat <- joint_pons
#For some reasons, there is now seurat@misc$colours and seurat@misc$colours_orig
seurat@misc$colours <- seurat@misc$colours_orig
# Convert cluster numbers to format used in levels(seurat@ident)
selected_clusters <- c(20, 13, 15, 3, 6, 11)
selected_clusters <- paste0("^", selected_clusters, "-")
selected_clusters <- grep(paste(selected_clusters,collapse="|"), levels(seurat@ident), value=TRUE)
# Colour vector is not available in this object for these cluster IDs, so they must be recovered a saved object. seurat@misc$colours and seurat@misc$colours_orig are identical vectors. Bug will be fixed later, according to Selin.
# First, recover corresponding new cluster ID.
load("/mnt/KLEINMAN_SCRATCH/projects/sjessa/from_hydra/single_cell/2019-02_revision1/output/atlas-02/palettes_joint.Rda")
seurat@misc$colours <- pal_jp
# Cluster columns also need to be renamed.
seurat@meta.data$cluster <- as.character(seurat@meta.data$cluster_joint)
monocle <- seurat_to_monocle(seurat, selected_clusters)
#monocle <- orderCells(monocle, reverse=TRUE)
colours <- monocle@experimentData@other$colours
p <- plot_cell_trajectory(monocle, color_by="cluster", show_branch_points=FALSE) + scale_color_manual(values=colours)
p <- p + theme(legend.title=element_blank())
show(p)
p <- p + facet_wrap(~cluster) + theme(legend.position = "none")
show(p)
plot_cell_trajectory(monocle, color_by="Pseudotime", show_branch_points = TRUE)
plot_cell_trajectory(monocle, color_by="State", show_branch_points=TRUE)
p <- plot_complex_cell_trajectory(monocle, color_by="cluster", show_branch_points=FALSE) + scale_color_manual(values=colours)
p <- p + theme(legend.title=element_blank())
show(p)
diff_test_res_all_genes <- differentialGeneTest(monocle,
fullModelFormulaStr = "~sm.ns(Pseudotime)", cores=12)
sig_gene_names_all_genes <- row.names(subset(diff_test_res_all_genes, qval < 0.1))
plot_pseudotime_heatmap(monocle[sig_gene_names_all_genes,],
cores = 12,
num_clusters=1,
show_rownames = FALSE)
diff_test_res_all_genes <- diff_test_res_all_genes %>% rownames_to_column("gene")
write.table(diff_test_res_all_genes, file.path(tables_directory, "5-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6_11_diff_test_res_all_genes.txt"), sep="\t", quote=FALSE, row.names = FALSE)
input_directory <- "/mnt/KLEINMAN_SCRATCH/projects/blancha/analyses/njabado/single_cell/annotation/animaltfdb3.0"
input_file <- "Mus_musculus_TF.txt"
transcription_factors <- read_tsv(file.path(input_directory, input_file), col_types = cols())
significant_genes_q_value_5_10_minus_5 <- filter(diff_test_res_all_genes, qval < 5*10^-5) %>% .$gene
cat("Number of significant genes: ", length(significant_genes_q_value_5_10_minus_5))
## Number of significant genes: 4944
significant_transcription_factors_q_value_5_10_minus_5 <- as.character(significant_genes_q_value_5_10_minus_5[significant_genes_q_value_5_10_minus_5 %in% transcription_factors$Symbol])
cat("Number of significant transcription factors:", length(significant_transcription_factors_q_value_5_10_minus_5))
## Number of significant transcription factors: 311
plot_genes_heatmap_output_q_value_5_10_minus_5 <- plot_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_5_10_minus_5,], cluster_rows=TRUE, num_clusters=3, return_heatmap=TRUE, show_rownames = TRUE)
plot_genes_heatmap_output_q_value_5_10_minus_5 <- plot_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_5_10_minus_5,], cluster_rows=TRUE, num_clusters=1, return_heatmap=TRUE, show_rownames = TRUE)
# The RMarkdown PDF has issues, hence this custom function to save the PDF file.
save_pheatmap_pdf(plot_genes_heatmap_output_q_value_5_10_minus_5[[2]], file.path("figures", "5-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6_11", "diff_test_res_plots_transcription_factors_only_q_value_5_10_minus_5_heatmap_custom.pdf"), width=16, height=36)
## pdf
## 2
heatmap_matrix_q_value_5_10_minus_5 <- plot_genes_heatmap_output_q_value_5_10_minus_5[[1]]
ph_res_q_value_5_10_minus_5 <- plot_genes_heatmap_output_q_value_5_10_minus_5[[2]]
pheatmap_ordering_q_value_5_10_minus_5 <- rownames(heatmap_matrix_q_value_5_10_minus_5[ph_res_q_value_5_10_minus_5$tree_row[["order"]],])
transcription_factors_table_q_value_5_10_minus_5 <- filter(diff_test_res_all_genes, gene %in% significant_transcription_factors_q_value_5_10_minus_5)
# Put genes from the transcription factor table in the same order
transcription_factors_table_q_value_5_10_minus_5 <- transcription_factors_table_q_value_5_10_minus_5 %>% arrange(match(gene, pheatmap_ordering_q_value_5_10_minus_5))
write.table(transcription_factors_table_q_value_5_10_minus_5, file.path(tables_directory, "5-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6_11-significant_transcription_factors_diff_test_analysis_qval_5_10_minus_5.txt"), sep="\t", quote=FALSE, row.names=FALSE)
heatmap_matrix_q_value_5_10_minus_5 <- plot_genes_heatmap_output_q_value_5_10_minus_5[[1]]
heatmap_matrix_q_value_5_10_minus_5 <- as.data.frame(heatmap_matrix_q_value_5_10_minus_5) %>% rownames_to_column("gene")
heatmap_matrix_q_value_5_10_minus_5 <- heatmap_matrix_q_value_5_10_minus_5 %>% arrange(match(gene, pheatmap_ordering_q_value_5_10_minus_5))
heatmap_matrix_q_value_5_10_minus_5 %>% head(20) %>% kable() %>% kable_styling() %>% scroll_box(height="200px", width="600px")
| gene | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Id3 | -1.1437784 | -1.0989690 | -1.0540253 | -1.0089629 | -0.9637975 | -0.9185447 | -0.8732207 | -0.8278417 | -0.7824240 | -0.7369842 | -0.6915390 | -0.6461053 | -0.6007001 | -0.5553406 | -0.5100441 | -0.4648281 | -0.4197103 | -0.3747084 | -0.3298402 | -0.2851239 | -0.2405774 | -0.1962192 | -0.1520675 | -0.1081409 | -0.0644578 | -0.0210370 | 0.0221028 | 0.0649427 | 0.1074638 | 0.1496471 | 0.1914735 | 0.2329238 | 0.2739790 | 0.3146196 | 0.3548263 | 0.3945799 | 0.4338609 | 0.4726498 | 0.5109271 | 0.5486734 | 0.5858691 | 0.6224947 | 0.6585306 | 0.6939572 | 0.7287549 | 0.7629042 | 0.7963854 | 0.8291790 | 0.8612655 | 0.8926253 | 0.9232331 | 0.9529433 | 0.9814938 | 1.0086167 | 1.0340435 | 1.0575046 | 1.0787301 | 1.0974497 | 1.1133930 | 1.1262901 | 1.1358713 | 1.1418682 | 1.1440132 | 1.1420408 | 1.1356873 | 1.1246917 | 1.1087961 | 1.0877460 | 1.0612913 | 1.0291869 | 0.9911929 | 0.9470761 | 0.8966104 | 0.8395778 | 0.7757695 | 0.7049871 | 0.6270437 | 0.5417652 | 0.4489923 | 0.3485815 | 0.2404074 | 0.1243647 | 0.0003702 | -0.1316346 | -0.2716806 | -0.4197687 | -0.5758662 | -0.7398891 | -0.9112727 | -1.0889214 | -1.2717184 | -1.4585612 | -1.6483677 | -1.8400814 | -2.0326782 | -2.2251720 | -2.4166207 | -2.6061315 | -2.7928663 | -2.9760462 |
| Zfp706 | -0.0765897 | -0.0367229 | 0.0031568 | 0.0429950 | 0.0827369 | 0.1223276 | 0.1617117 | 0.2008333 | 0.2396363 | 0.2780644 | 0.3160609 | 0.3535686 | 0.3905303 | 0.4268884 | 0.4625849 | 0.4975617 | 0.5317605 | 0.5651226 | 0.5975893 | 0.6291017 | 0.6596006 | 0.6890267 | 0.7173207 | 0.7444232 | 0.7702746 | 0.7948153 | 0.8179860 | 0.8397269 | 0.8599787 | 0.8786819 | 0.8957773 | 0.9112057 | 0.9249083 | 0.9368263 | 0.9469012 | 0.9550749 | 0.9612896 | 0.9654879 | 0.9676127 | 0.9676074 | 0.9654160 | 0.9609831 | 0.9542536 | 0.9451735 | 0.9336891 | 0.9197476 | 0.9032970 | 0.8842863 | 0.8626651 | 0.8383843 | 0.8113982 | 0.7817161 | 0.7494001 | 0.7145148 | 0.6771253 | 0.6372972 | 0.5950965 | 0.5505898 | 0.5038436 | 0.4549249 | 0.4039011 | 0.3508394 | 0.2958074 | 0.2388727 | 0.1801030 | 0.1195658 | 0.0573289 | -0.0065404 | -0.0719745 | -0.1389063 | -0.2072688 | -0.2769951 | -0.3480188 | -0.4202737 | -0.4936939 | -0.5682139 | -0.6437688 | -0.7202938 | -0.7977250 | -0.8759986 | -0.9550516 | -1.0348215 | -1.1152463 | -1.1962648 | -1.2778162 | -1.3598406 | -1.4422786 | -1.5250717 | -1.6081603 | -1.6914843 | -1.7749841 | -1.8586009 | -1.9422770 | -2.0259553 | -2.1095796 | -2.1930948 | -2.2764465 | -2.3595812 | -2.4424465 | -2.5249907 |
| Id1 | 1.4871422 | 1.4381725 | 1.3894833 | 1.3411226 | 1.2931377 | 1.2455749 | 1.1984795 | 1.1518958 | 1.1058674 | 1.0604368 | 1.0156456 | 0.9715347 | 0.9281439 | 0.8855122 | 0.8436780 | 0.8026786 | 0.7625507 | 0.7233304 | 0.6850529 | 0.6477527 | 0.6114640 | 0.5762202 | 0.5420543 | 0.5089987 | 0.4770855 | 0.4463464 | 0.4168129 | 0.3885160 | 0.3614870 | 0.3357566 | 0.3113557 | 0.2883152 | 0.2666661 | 0.2464396 | 0.2276672 | 0.2103805 | 0.1946119 | 0.1803940 | 0.1677600 | 0.1567441 | 0.1473808 | 0.1397059 | 0.1337558 | 0.1295683 | 0.1271821 | 0.1266372 | 0.1279752 | 0.1312388 | 0.1364727 | 0.1437230 | 0.1530277 | 0.1642137 | 0.1769041 | 0.1907122 | 0.2052487 | 0.2201220 | 0.2349368 | 0.2492952 | 0.2627959 | 0.2750354 | 0.2856078 | 0.2941061 | 0.3001230 | 0.3032521 | 0.3030896 | 0.2992353 | 0.2912950 | 0.2788825 | 0.2616214 | 0.2391483 | 0.2111148 | 0.1771908 | 0.1370677 | 0.0904614 | 0.0371163 | -0.0231912 | -0.0906488 | -0.1654039 | -0.2475593 | -0.3371692 | -0.4342341 | -0.5386972 | -0.6504391 | -0.7692745 | -0.8949478 | -1.0271304 | -1.1654176 | -1.3093116 | -1.4577780 | -1.6092531 | -1.7622270 | -1.9152926 | -2.0671595 | -2.2166656 | -2.3627842 | -2.5046291 | -2.6414553 | -2.7726568 | -2.8977616 | -3.0000000 |
| Msx2 | 1.2595102 | 1.2236724 | 1.1881777 | 1.1530591 | 1.1183487 | 1.0840771 | 1.0502741 | 1.0169680 | 0.9841864 | 0.9519556 | 0.9203010 | 0.8892473 | 0.8588179 | 0.8290356 | 0.7999225 | 0.7714997 | 0.7437877 | 0.7168065 | 0.6905755 | 0.6651133 | 0.6404384 | 0.6165687 | 0.5935217 | 0.5713147 | 0.5499647 | 0.5294887 | 0.5099033 | 0.4912253 | 0.4734715 | 0.4566586 | 0.4408036 | 0.4259237 | 0.4120364 | 0.3991596 | 0.3873115 | 0.3765109 | 0.3667772 | 0.3581305 | 0.3505915 | 0.3441820 | 0.3389245 | 0.3348426 | 0.3319609 | 0.3303056 | 0.3299037 | 0.3307839 | 0.3329766 | 0.3365135 | 0.3414283 | 0.3477566 | 0.3555239 | 0.3644971 | 0.3741921 | 0.3841093 | 0.3937433 | 0.4025829 | 0.4101117 | 0.4158099 | 0.4191568 | 0.4196341 | 0.4167297 | 0.4099428 | 0.3987892 | 0.3828077 | 0.3615669 | 0.3346723 | 0.3017738 | 0.2625735 | 0.2168333 | 0.1643824 | 0.1051237 | 0.0390406 | -0.0337983 | -0.1132353 | -0.1990211 | -0.2908140 | -0.3881817 | -0.4906037 | -0.5974778 | -0.7081267 | -0.8218084 | -0.9377277 | -1.0550496 | -1.1729142 | -1.2904527 | -1.4068041 | -1.5211318 | -1.6326299 | -1.7402677 | -1.8428948 | -1.9396463 | -2.0299386 | -2.1134371 | -2.1900192 | -2.2597371 | -2.3227815 | -2.3794476 | -2.4301048 | -2.4751708 | -2.5150894 |
| Tgif1 | 2.1439933 | 2.0366318 | 1.9320509 | 1.8302014 | 1.7310339 | 1.6344987 | 1.5405458 | 1.4491253 | 1.3601872 | 1.2736814 | 1.1895579 | 1.1077670 | 1.0282588 | 0.9509840 | 0.8758935 | 0.8029382 | 0.7320699 | 0.6632404 | 0.5964022 | 0.5315080 | 0.4685112 | 0.4073659 | 0.3480264 | 0.2904479 | 0.2345862 | 0.1803975 | 0.1278389 | 0.0768682 | 0.0274437 | -0.0204754 | -0.0669293 | -0.1119574 | -0.1555983 | -0.1978901 | -0.2388699 | -0.2785741 | -0.3170385 | -0.3542979 | -0.3903866 | -0.4253379 | -0.4591846 | -0.4919585 | -0.5236909 | -0.5544122 | -0.5841522 | -0.6129397 | -0.6408032 | -0.6677703 | -0.6938677 | -0.7191217 | -0.7435548 | -0.7671243 | -0.7897362 | -0.8113088 | -0.8317743 | -0.8510769 | -0.8691709 | -0.8860190 | -0.9015905 | -0.9158596 | -0.9288035 | -0.9404006 | -0.9506291 | -0.9594650 | -0.9668803 | -0.9728413 | -0.9773066 | -0.9802249 | -0.9815328 | -0.9811523 | -0.9789877 | -0.9749221 | -0.9688136 | -0.9604904 | -0.9497451 | -0.9363279 | -0.9199383 | -0.9002146 | -0.8767217 | -0.8489355 | -0.8162240 | -0.7778240 | -0.7328113 | -0.6800650 | -0.6182221 | -0.5456213 | -0.4602327 | -0.3595837 | -0.2410453 | -0.1019992 | 0.0604966 | 0.2497240 | 0.4692814 | 0.7230333 | 1.0150297 | 1.3493874 | 1.7301310 | 2.1609933 | 2.6451815 | 3.0000000 |
| Foxp1 | 1.6557190 | 1.6060392 | 1.5567228 | 1.5077478 | 1.4590928 | 1.4107369 | 1.3626600 | 1.3148425 | 1.2672655 | 1.2199106 | 1.1727602 | 1.1257971 | 1.0790049 | 1.0323676 | 0.9858701 | 0.9394976 | 0.8932361 | 0.8470721 | 0.8009928 | 0.7549860 | 0.7090400 | 0.6631438 | 0.6172870 | 0.5714597 | 0.5256529 | 0.4798578 | 0.4340666 | 0.3882719 | 0.3424670 | 0.2966457 | 0.2508025 | 0.2049325 | 0.1590316 | 0.1130960 | 0.0671227 | 0.0211094 | -0.0249458 | -0.0710440 | -0.1171858 | -0.1633711 | -0.2095991 | -0.2558687 | -0.3021778 | -0.3485241 | -0.3949042 | -0.4413147 | -0.4877511 | -0.5342086 | -0.5806816 | -0.6271643 | -0.6736432 | -0.7199615 | -0.7658355 | -0.8109918 | -0.8551725 | -0.8981347 | -0.9396499 | -0.9795026 | -1.0174892 | -1.0534171 | -1.0871025 | -1.1183692 | -1.1470465 | -1.1729677 | -1.1959676 | -1.2158806 | -1.2325383 | -1.2457670 | -1.2553848 | -1.2611993 | -1.2630039 | -1.2605749 | -1.2536677 | -1.2420127 | -1.2253111 | -1.2032300 | -1.1753968 | -1.1413933 | -1.1007489 | -1.0529329 | -0.9973460 | -0.9333101 | -0.8600580 | -0.7767204 | -0.6823120 | -0.5757159 | -0.4556652 | -0.3207404 | -0.1698787 | -0.0025627 | 0.1816901 | 0.3833365 | 0.6027817 | 0.8403502 | 1.0962574 | 1.3705784 | 1.6632177 | 1.9738789 | 2.3020362 | 2.6469083 |
| Creb5 | 2.1349100 | 2.0546172 | 1.9755574 | 1.8977084 | 1.8210484 | 1.7455560 | 1.6712105 | 1.5979915 | 1.5258792 | 1.4548542 | 1.3848976 | 1.3159909 | 1.2481160 | 1.1812553 | 1.1153916 | 1.0505081 | 0.9865884 | 0.9236165 | 0.8615768 | 0.8004539 | 0.7402330 | 0.6808996 | 0.6224394 | 0.5648385 | 0.5080834 | 0.4521610 | 0.3970582 | 0.3427626 | 0.2892617 | 0.2365436 | 0.1845966 | 0.1334091 | 0.0829701 | 0.0332686 | -0.0157062 | -0.0639645 | -0.1115166 | -0.1583724 | -0.2045417 | -0.2500339 | -0.2948583 | -0.3390240 | -0.3825399 | -0.4254146 | -0.4676565 | -0.5092741 | -0.5502754 | -0.5906683 | -0.6304606 | -0.6696598 | -0.7082688 | -0.7461926 | -0.7832517 | -0.8192775 | -0.8541147 | -0.8876210 | -0.9196653 | -0.9501269 | -0.9788939 | -1.0058621 | -1.0309331 | -1.0540132 | -1.0750113 | -1.0938378 | -1.1104026 | -1.1246130 | -1.1363723 | -1.1455777 | -1.1521179 | -1.1558709 | -1.1567016 | -1.1544592 | -1.1489737 | -1.1400531 | -1.1274791 | -1.1110032 | -1.0903417 | -1.0651702 | -1.0351168 | -0.9997552 | -0.9585957 | -0.9110750 | -0.8565450 | -0.7942584 | -0.7233527 | -0.6428314 | -0.5515411 | -0.4481582 | -0.3315589 | -0.2009699 | -0.0555918 | 0.1054097 | 0.2828846 | 0.4776757 | 0.6905926 | 0.9223810 | 1.1736884 | 1.4450252 | 1.7367229 | 2.0488892 |
| Jund | 1.8228545 | 1.7698572 | 1.7170161 | 1.6643276 | 1.6117884 | 1.5593947 | 1.5071432 | 1.4550304 | 1.4030531 | 1.3512078 | 1.2994914 | 1.2479006 | 1.1964324 | 1.1450836 | 1.0938511 | 1.0427322 | 0.9917237 | 0.9408229 | 0.8900270 | 0.8393332 | 0.7887388 | 0.7382412 | 0.6878379 | 0.6375263 | 0.5873040 | 0.5371686 | 0.4871178 | 0.4371494 | 0.3872611 | 0.3374509 | 0.2877166 | 0.2380563 | 0.1884680 | 0.1389499 | 0.0895002 | 0.0401171 | -0.0092010 | -0.0584558 | -0.1076486 | -0.1567811 | -0.2058545 | -0.2548703 | -0.3038295 | -0.3527335 | -0.4015833 | -0.4503799 | -0.4991242 | -0.5478172 | -0.5964597 | -0.6450523 | -0.6935896 | -0.7419359 | -0.7898343 | -0.8370276 | -0.8832637 | -0.9282952 | -0.9718796 | -1.0137784 | -1.0537572 | -1.0915853 | -1.1270348 | -1.1598804 | -1.1898987 | -1.2168671 | -1.2405635 | -1.2607653 | -1.2772482 | -1.2897855 | -1.2981469 | -1.3020973 | -1.3013957 | -1.2957936 | -1.2850342 | -1.2688506 | -1.2469644 | -1.2190840 | -1.1849035 | -1.1441006 | -1.0963351 | -1.0412473 | -0.9784559 | -0.9075569 | -0.8281213 | -0.7396936 | -0.6417904 | -0.5338984 | -0.4154732 | -0.2859534 | -0.1452241 | 0.0062696 | 0.1680244 | 0.3395044 | 0.5201350 | 0.7092985 | 0.9063304 | 1.1105170 | 1.3210929 | 1.5372408 | 1.7580911 | 1.9827225 |
| Msx1 | 0.6377484 | 0.6556217 | 0.6735028 | 0.6912847 | 0.7088579 | 0.7261101 | 0.7429269 | 0.7591913 | 0.7747845 | 0.7895856 | 0.8034722 | 0.8163209 | 0.8280071 | 0.8384060 | 0.8473928 | 0.8548433 | 0.8606343 | 0.8646445 | 0.8667549 | 0.8668495 | 0.8648162 | 0.8605473 | 0.8539407 | 0.8449001 | 0.8333362 | 0.8191676 | 0.8023214 | 0.7827339 | 0.7603519 | 0.7351330 | 0.7070467 | 0.6760748 | 0.6422123 | 0.6054679 | 0.5658646 | 0.5234399 | 0.4782464 | 0.4303522 | 0.3798405 | 0.3268100 | 0.2713746 | 0.2136633 | 0.1538195 | 0.0920006 | 0.0283773 | -0.0368675 | -0.1035394 | -0.1714341 | -0.2403386 | -0.3100326 | -0.3802772 | -0.4505705 | -0.5202163 | -0.5885994 | -0.6551946 | -0.7195632 | -0.7813477 | -0.8402650 | -0.8960990 | -0.9486925 | -0.9979391 | -1.0437746 | -1.0861695 | -1.1251206 | -1.1606443 | -1.1927696 | -1.2215313 | -1.2469643 | -1.2690979 | -1.2879497 | -1.3035209 | -1.3157898 | -1.3247063 | -1.3301853 | -1.3320989 | -1.3302679 | -1.3244517 | -1.3143346 | -1.2995110 | -1.2794652 | -1.2535465 | -1.2209377 | -1.1806150 | -1.1312956 | -1.0713714 | -0.9988225 | -0.9111051 | -0.8050235 | -0.6771466 | -0.5240275 | -0.3416581 | -0.1254067 | 0.1299906 | 0.4304062 | 0.7822519 | 1.1923480 | 1.6677175 | 2.2152932 | 2.8415351 | 3.0000000 |
| Peg3 | 1.3950153 | 1.3768095 | 1.3585907 | 1.3403065 | 1.3219051 | 1.3033353 | 1.2845462 | 1.2654875 | 1.2461095 | 1.2263628 | 1.2061986 | 1.1855689 | 1.1644261 | 1.1427233 | 1.1204142 | 1.0974534 | 1.0737961 | 1.0493983 | 1.0242169 | 0.9982096 | 0.9713352 | 0.9435534 | 0.9148250 | 0.8851117 | 0.8543767 | 0.8225842 | 0.7896999 | 0.7556906 | 0.7205247 | 0.6841722 | 0.6466044 | 0.6077945 | 0.5677173 | 0.5263495 | 0.4836695 | 0.4396577 | 0.3942966 | 0.3475708 | 0.2994670 | 0.2499740 | 0.1990832 | 0.1467882 | 0.0930851 | 0.0379725 | -0.0185484 | -0.0764737 | -0.1357970 | -0.1965089 | -0.2585974 | -0.3220474 | -0.3868312 | -0.4527089 | -0.5192490 | -0.5860297 | -0.6526467 | -0.7187143 | -0.7838644 | -0.8477471 | -0.9100296 | -0.9703954 | -1.0285433 | -1.0841865 | -1.1370506 | -1.1868725 | -1.2333983 | -1.2763815 | -1.3155805 | -1.3507572 | -1.3816735 | -1.4080894 | -1.4297602 | -1.4464329 | -1.4578438 | -1.4637148 | -1.4637495 | -1.4576295 | -1.4450103 | -1.4255163 | -1.3987358 | -1.3642158 | -1.3214555 | -1.2698998 | -1.2089321 | -1.1378656 | -1.0559349 | -0.9622856 | -0.8559632 | -0.7359198 | -0.6015769 | -0.4529948 | -0.2902813 | -0.1135720 | 0.0769513 | 0.2810436 | 0.4983787 | 0.7285321 | 0.9709647 | 1.2250072 | 1.4898461 | 1.7645113 |
| Hes1 | 1.5270416 | 1.5025261 | 1.4780026 | 1.4534345 | 1.4287855 | 1.4040193 | 1.3790999 | 1.3539913 | 1.3286580 | 1.3030645 | 1.2771753 | 1.2509555 | 1.2243702 | 1.1973847 | 1.1699645 | 1.1420755 | 1.1136837 | 1.0847554 | 1.0552570 | 1.0251555 | 0.9944179 | 0.9630116 | 0.9309044 | 0.8980643 | 0.8644597 | 0.8300592 | 0.7948321 | 0.7587478 | 0.7217762 | 0.6838877 | 0.6450530 | 0.6052433 | 0.5644305 | 0.5225867 | 0.4796846 | 0.4356977 | 0.3905998 | 0.3443653 | 0.2969695 | 0.2483880 | 0.1985974 | 0.1475746 | 0.0952977 | 0.0417453 | -0.0131032 | -0.0692676 | -0.1267668 | -0.1856187 | -0.2458405 | -0.3074484 | -0.3704486 | -0.4346582 | -0.4997168 | -0.5652621 | -0.6309373 | -0.6963913 | -0.7612788 | -0.8252602 | -0.8880017 | -0.9491747 | -1.0084561 | -1.0655275 | -1.1200752 | -1.1717893 | -1.2203635 | -1.2654942 | -1.3068799 | -1.3442203 | -1.3772158 | -1.4055659 | -1.4289688 | -1.4471198 | -1.4597106 | -1.4664275 | -1.4669506 | -1.4609519 | -1.4480944 | -1.4280299 | -1.4003977 | -1.3648229 | -1.3209145 | -1.2682638 | -1.2064420 | -1.1349988 | -1.0534597 | -0.9613245 | -0.8580648 | -0.7431397 | -0.6165286 | -0.4788488 | -0.3307659 | -0.1729634 | -0.0061478 | 0.1689471 | 0.3515562 | 0.5408799 | 0.7360812 | 0.9362840 | 1.1405711 | 1.3479837 |
| Jun | -0.2299473 | -0.1659870 | -0.1019971 | -0.0380964 | 0.0255949 | 0.0889557 | 0.1518637 | 0.2141958 | 0.2758280 | 0.3366353 | 0.3964919 | 0.4552710 | 0.5128454 | 0.5690868 | 0.6238666 | 0.6770553 | 0.7285232 | 0.7781400 | 0.8257749 | 0.8712971 | 0.9145753 | 0.9554783 | 0.9938747 | 1.0296333 | 1.0626229 | 1.0927126 | 1.1197720 | 1.1436709 | 1.1642799 | 1.1814701 | 1.1951135 | 1.2050831 | 1.2112529 | 1.2134980 | 1.2116949 | 1.2057218 | 1.1954582 | 1.1807857 | 1.1615875 | 1.1377494 | 1.1091593 | 1.0757074 | 1.0372871 | 0.9937943 | 0.9451284 | 0.8911918 | 0.8318909 | 0.7671358 | 0.6968407 | 0.6209245 | 0.5393272 | 0.4523487 | 0.3606283 | 0.2648146 | 0.1655514 | 0.0634760 | -0.0407812 | -0.1465971 | -0.2533571 | -0.3604552 | -0.4672942 | -0.5732864 | -0.6778533 | -0.7804258 | -0.8804439 | -0.9773565 | -1.0706207 | -1.1597015 | -1.2440709 | -1.3232071 | -1.3965930 | -1.4637155 | -1.5240640 | -1.5771286 | -1.6223985 | -1.6593604 | -1.6874962 | -1.7062809 | -1.7151807 | -1.7136502 | -1.7011299 | -1.6770438 | -1.6407968 | -1.5917715 | -1.5293256 | -1.4527894 | -1.3614621 | -1.2546354 | -1.1323688 | -0.9956466 | -0.8455124 | -0.6830225 | -0.5092526 | -0.3253024 | -0.1323006 | 0.0685918 | 0.2761784 | 0.4892262 | 0.7064635 | 0.9265802 |
| Mafb | 1.4075855 | 1.3983572 | 1.3890850 | 1.3797053 | 1.3701554 | 1.3603731 | 1.3502966 | 1.3398650 | 1.3290180 | 1.3176962 | 1.3058409 | 1.2933942 | 1.2802995 | 1.2665010 | 1.2519443 | 1.2365760 | 1.2203443 | 1.2031989 | 1.1850910 | 1.1659736 | 1.1458017 | 1.1245322 | 1.1021242 | 1.0785391 | 1.0537407 | 1.0276955 | 1.0003727 | 0.9717444 | 0.9417856 | 0.9104747 | 0.8777931 | 0.8437259 | 0.8082617 | 0.7713927 | 0.7331151 | 0.6934286 | 0.6523374 | 0.6098493 | 0.5659766 | 0.5207357 | 0.4741471 | 0.4262358 | 0.3770308 | 0.3265657 | 0.2748781 | 0.2220098 | 0.1680071 | 0.1129198 | 0.0568022 | -0.0002880 | -0.0582827 | -0.1169799 | -0.1760635 | -0.2352331 | -0.2942098 | -0.3527360 | -0.4105758 | -0.4675137 | -0.5233549 | -0.5779235 | -0.6310625 | -0.6826320 | -0.7325082 | -0.7805822 | -0.8267586 | -0.8709540 | -0.9130960 | -0.9531212 | -0.9909743 | -1.0266064 | -1.0599737 | -1.0910359 | -1.1197553 | -1.1460946 | -1.1700164 | -1.1914810 | -1.2104457 | -1.2268625 | -1.2406773 | -1.2518279 | -1.2602424 | -1.2658372 | -1.2685155 | -1.2681644 | -1.2646531 | -1.2578299 | -1.2475191 | -1.2335241 | -1.2158079 | -1.1945361 | -1.1698771 | -1.1419959 | -1.1110582 | -1.0772361 | -1.0407122 | -1.0016845 | -0.9603701 | -0.9170097 | -0.8718711 | -0.8252529 |
| Smarca1 | 0.9527755 | 0.9684955 | 0.9841820 | 0.9997492 | 1.0151098 | 1.0301758 | 1.0448581 | 1.0590665 | 1.0727101 | 1.0856972 | 1.0979353 | 1.1093316 | 1.1197926 | 1.1292248 | 1.1375346 | 1.1446285 | 1.1504133 | 1.1547965 | 1.1576864 | 1.1589923 | 1.1586249 | 1.1564965 | 1.1525215 | 1.1466162 | 1.1386999 | 1.1286945 | 1.1165252 | 1.1021209 | 1.0854145 | 1.0663430 | 1.0448482 | 1.0208770 | 0.9943817 | 0.9653202 | 0.9336567 | 0.8993618 | 0.8624129 | 0.8227945 | 0.7804986 | 0.7355246 | 0.6878804 | 0.6375815 | 0.5846522 | 0.5291252 | 0.4710421 | 0.4104531 | 0.3474174 | 0.2820030 | 0.2142869 | 0.1443549 | 0.0723116 | -0.0015147 | -0.0766040 | -0.1524567 | -0.2286045 | -0.3046110 | -0.3800722 | -0.4546167 | -0.5279048 | -0.5996277 | -0.6695067 | -0.7372907 | -0.8027554 | -0.8657004 | -0.9259477 | -0.9833390 | -1.0377332 | -1.0890041 | -1.1370379 | -1.1817302 | -1.2229839 | -1.2607058 | -1.2948045 | -1.3251872 | -1.3517571 | -1.3744102 | -1.3930324 | -1.4074960 | -1.4176565 | -1.4233487 | -1.4243824 | -1.4205385 | -1.4115632 | -1.3971630 | -1.3769980 | -1.3506747 | -1.3177376 | -1.2776706 | -1.2302300 | -1.1755357 | -1.1137144 | -1.0448879 | -0.9691855 | -0.8867554 | -0.7977758 | -0.7024675 | -0.6011050 | -0.4940283 | -0.3816547 | -0.2644893 |
| Camta1 | 1.9425858 | 1.8980164 | 1.8535802 | 1.8092645 | 1.7650564 | 1.7209435 | 1.6769135 | 1.6329542 | 1.5890535 | 1.5451998 | 1.5013811 | 1.4575862 | 1.4138036 | 1.3700221 | 1.3262307 | 1.2824186 | 1.2385751 | 1.1946897 | 1.1507521 | 1.1067521 | 1.0626798 | 1.0185252 | 0.9742787 | 0.9299310 | 0.8854726 | 0.8408946 | 0.7961878 | 0.7513437 | 0.7063537 | 0.6612093 | 0.6159024 | 0.5704249 | 0.5247692 | 0.4789274 | 0.4328924 | 0.3866567 | 0.3402134 | 0.2935558 | 0.2466770 | 0.1995709 | 0.1522311 | 0.1046517 | 0.0568269 | 0.0087512 | -0.0395808 | -0.0881742 | -0.1370339 | -0.1861645 | -0.2355705 | -0.2852560 | -0.3352208 | -0.3853731 | -0.4355362 | -0.4855330 | -0.5351901 | -0.5843373 | -0.6328078 | -0.6804383 | -0.7270683 | -0.7725405 | -0.8167005 | -0.8593965 | -0.9004791 | -0.9398009 | -0.9772168 | -1.0125830 | -1.0457570 | -1.0765974 | -1.1049633 | -1.1307137 | -1.1537077 | -1.1738035 | -1.1908581 | -1.2047270 | -1.2152633 | -1.2223172 | -1.2257359 | -1.2253624 | -1.2210351 | -1.2125871 | -1.1998453 | -1.1826302 | -1.1607542 | -1.1340217 | -1.1022275 | -1.0651562 | -1.0225811 | -0.9742719 | -0.9202595 | -0.8608907 | -0.7965323 | -0.7275558 | -0.6543392 | -0.5772690 | -0.4967422 | -0.4131672 | -0.3269660 | -0.2385749 | -0.1484453 | -0.0570451 |
| E2f5 | 1.8562881 | 1.8165953 | 1.7770033 | 1.7375020 | 1.6980815 | 1.6587318 | 1.6194432 | 1.5802061 | 1.5410110 | 1.5018485 | 1.4627093 | 1.4235841 | 1.3844639 | 1.3453398 | 1.3062028 | 1.2670443 | 1.2278557 | 1.1886283 | 1.1493538 | 1.1100239 | 1.0706305 | 1.0311655 | 0.9916209 | 0.9519890 | 0.9122619 | 0.8724322 | 0.8324924 | 0.7924352 | 0.7522532 | 0.7119395 | 0.6714870 | 0.6308889 | 0.5901386 | 0.5492293 | 0.5081546 | 0.4669083 | 0.4254841 | 0.3838760 | 0.3420780 | 0.3000843 | 0.2578893 | 0.2154875 | 0.1728735 | 0.1300422 | 0.0869883 | 0.0437070 | 0.0001935 | -0.0435568 | -0.0875485 | -0.1317858 | -0.1762703 | -0.2209488 | -0.2657165 | -0.3104682 | -0.3551003 | -0.3995109 | -0.4435996 | -0.4872679 | -0.5304185 | -0.5729561 | -0.6147865 | -0.6558172 | -0.6959571 | -0.7351162 | -0.7732060 | -0.8101390 | -0.8458288 | -0.8801898 | -0.9131376 | -0.9445882 | -0.9744582 | -1.0026648 | -1.0291255 | -1.0537578 | -1.0764793 | -1.0972076 | -1.1158596 | -1.1323520 | -1.1466005 | -1.1585203 | -1.1680249 | -1.1750271 | -1.1794375 | -1.1811654 | -1.1801177 | -1.1761992 | -1.1693121 | -1.1593605 | -1.1463978 | -1.1306536 | -1.1123665 | -1.0917752 | -1.0691186 | -1.0446365 | -1.0185701 | -0.9911624 | -0.9626587 | -0.9333065 | -0.9033562 | -0.8730609 |
| Dmrtb1 | 1.8338638 | 1.8052919 | 1.7768570 | 1.7484327 | 1.7198971 | 1.6911332 | 1.6620292 | 1.6324782 | 1.6023785 | 1.5716339 | 1.5401538 | 1.5078536 | 1.4746549 | 1.4404857 | 1.4052808 | 1.3689824 | 1.3315400 | 1.2929108 | 1.2530605 | 1.2119629 | 1.1696008 | 1.1259658 | 1.0810587 | 1.0348900 | 0.9874794 | 0.9388566 | 0.8890605 | 0.8381400 | 0.7861533 | 0.7331680 | 0.6792608 | 0.6245169 | 0.5690301 | 0.5129017 | 0.4562402 | 0.3991606 | 0.3417838 | 0.2842354 | 0.2266451 | 0.1691456 | 0.1118716 | 0.0549589 | -0.0014569 | -0.0572412 | -0.1122619 | -0.1663903 | -0.2195019 | -0.2714779 | -0.3222059 | -0.3715807 | -0.4195004 | -0.4657708 | -0.5101448 | -0.5524332 | -0.5925035 | -0.6302734 | -0.6657041 | -0.6987939 | -0.7295719 | -0.7580921 | -0.7844279 | -0.8086673 | -0.8309087 | -0.8512568 | -0.8698202 | -0.8867076 | -0.9020269 | -0.9158826 | -0.9283745 | -0.9395971 | -0.9496383 | -0.9585791 | -0.9664929 | -0.9734455 | -0.9794944 | -0.9846890 | -0.9890700 | -0.9926693 | -0.9955094 | -0.9976030 | -0.9989523 | -0.9995478 | -0.9993670 | -0.9983729 | -0.9965112 | -0.9937076 | -0.9898639 | -0.9848543 | -0.9785746 | -0.9709596 | -0.9619291 | -0.9513872 | -0.9392244 | -0.9253208 | -0.9095493 | -0.8917805 | -0.8718879 | -0.8497554 | -0.8252851 | -0.7984082 |
| Insm2 | 3.0000000 | 3.0000000 | 0.9472274 | 0.2060407 | -0.0320474 | -0.1078657 | -0.1320253 | -0.1397585 | -0.1422501 | -0.1430594 | -0.1433248 | -0.1434127 | -0.1434422 | -0.1434522 | -0.1434557 | -0.1434569 | -0.1434573 | -0.1434575 | -0.1434575 | -0.1434575 | -0.1434575 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434576 | -0.1434575 | -0.1434575 | -0.1434575 | -0.1434575 | -0.1434574 | -0.1434572 | -0.1434568 | -0.1434560 | -0.1434543 | -0.1434513 | -0.1434458 | -0.1434365 | -0.1434217 | -0.1433998 | -0.1433698 | -0.1433325 | -0.1432910 | -0.1432512 | -0.1432209 | -0.1432073 | -0.1432147 | -0.1432422 | -0.1432839 | -0.1433307 | -0.1433735 | -0.1434066 | -0.1434291 | -0.1434428 | -0.1434504 | -0.1434543 | -0.1434561 | -0.1434570 | -0.1434573 | -0.1434575 | -0.1434575 | -0.1434575 |
| Ptf1a | 3.0000000 | 3.0000000 | 2.6091697 | 1.3486412 | 0.6377661 | 0.2497108 | 0.0415442 | -0.0692320 | -0.1280417 | -0.1592946 | -0.1759552 | -0.1848774 | -0.1896825 | -0.1922873 | -0.1937096 | -0.1944925 | -0.1949271 | -0.1951707 | -0.1953085 | -0.1953874 | -0.1954330 | -0.1954597 | -0.1954755 | -0.1954850 | -0.1954907 | -0.1954943 | -0.1954965 | -0.1954979 | -0.1954988 | -0.1954994 | -0.1954998 | -0.1955001 | -0.1955002 | -0.1955004 | -0.1955005 | -0.1955005 | -0.1955006 | -0.1955006 | -0.1955006 | -0.1955006 | -0.1955007 | -0.1955007 | -0.1955007 | -0.1955007 | -0.1955007 | -0.1955007 | -0.1955007 | -0.1955006 | -0.1955006 | -0.1955006 | -0.1955005 | -0.1955005 | -0.1955004 | -0.1955002 | -0.1955000 | -0.1954997 | -0.1954991 | -0.1954983 | -0.1954970 | -0.1954950 | -0.1954918 | -0.1954865 | -0.1954782 | -0.1954647 | -0.1954431 | -0.1954087 | -0.1953541 | -0.1952684 | -0.1951354 | -0.1949323 | -0.1946274 | -0.1941792 | -0.1935360 | -0.1926378 | -0.1914219 | -0.1898330 | -0.1878383 | -0.1854466 | -0.1827279 | -0.1798286 | -0.1769735 | -0.1744496 | -0.1725675 | -0.1716051 | -0.1717444 | -0.1730215 | -0.1753049 | -0.1783140 | -0.1816371 | -0.1848554 | -0.1876848 | -0.1899890 | -0.1917508 | -0.1930283 | -0.1939138 | -0.1945048 | -0.1948868 | -0.1951273 | -0.1952756 | -0.1953657 |
| Neurod4 | 3.0000000 | 3.0000000 | 1.9479342 | 0.8438916 | 0.3106099 | 0.0549915 | -0.0672504 | -0.1257465 | -0.1538059 | -0.1673140 | -0.1738463 | -0.1770219 | -0.1785750 | -0.1793397 | -0.1797189 | -0.1799085 | -0.1800041 | -0.1800528 | -0.1800778 | -0.1800908 | -0.1800976 | -0.1801012 | -0.1801031 | -0.1801042 | -0.1801048 | -0.1801051 | -0.1801053 | -0.1801054 | -0.1801055 | -0.1801055 | -0.1801055 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801056 | -0.1801055 | -0.1801055 | -0.1801055 | -0.1801055 | -0.1801054 | -0.1801052 | -0.1801050 | -0.1801047 | -0.1801041 | -0.1801031 | -0.1801015 | -0.1800989 | -0.1800944 | -0.1800869 | -0.1800746 | -0.1800543 | -0.1800210 | -0.1799669 | -0.1798799 | -0.1797416 | -0.1795242 | -0.1791874 | -0.1786736 | -0.1779032 | -0.1767699 | -0.1751304 | -0.1727899 | -0.1694863 | -0.1648690 | -0.1584689 | -0.1496575 | -0.1375897 | -0.1211233 | -0.0987058 | -0.0682118 | -0.0267085 | 0.0298841 |
write.table(heatmap_matrix_q_value_5_10_minus_5, file = file.path(tables_directory, "5-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6_11-significant_transcription_factors_diff_test_analysis_qval_5_10_minus_5_heatmap_matrix.txt"), sep="\t", quote=FALSE, row.names=FALSE)
significant_genes_q_value_0.01 <- filter(diff_test_res_all_genes, qval < 0.01) %>% .$gene
cat("Number of significant genes: ", length(significant_genes_q_value_0.01))
## Number of significant genes: 7245
significant_transcription_factors_q_value_0.01 <- as.character(significant_genes_q_value_0.01[significant_genes_q_value_0.01 %in% transcription_factors$Symbol])
cat("Number of significant transcription factors:", length(significant_transcription_factors_q_value_0.01))
## Number of significant transcription factors: 474
plot_genes_heatmap_output_q_value_0.01 <- plot_pseudotime_heatmap(monocle[significant_transcription_factors_q_value_0.01,], cluster_rows=TRUE, num_clusters=1, return_heatmap=TRUE, show_rownames = TRUE)
## <simpleError in checkwz(wz, M = M, trace = trace, wzepsilon = control$wzepsilon): NAs found in the working weights variable 'wz'>
save_pheatmap_pdf(plot_genes_heatmap_output_q_value_0.01[[2]], file.path("figures", "5-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6_11", "diff_test_plots_transcription_factors_only_q_value_0.01_heatmap_custom.pdf"), width=16, height=40)
## pdf
## 2
heatmap_matrix_q_value_0.01 <- plot_genes_heatmap_output_q_value_0.01[[1]]
ph_res_q_value_0.01 <- plot_genes_heatmap_output_q_value_0.01[[2]]
pheatmap_ordering_q_value_0.01 <- rownames(heatmap_matrix_q_value_0.01[ph_res_q_value_0.01$tree_row[["order"]],])
transcription_factors_table_q_value_0.01 <- filter(diff_test_res_all_genes, gene %in% significant_transcription_factors_q_value_0.01)
# Put genes from the transcription factor table in the same order
transcription_factors_table_q_value_0.01 <- transcription_factors_table_q_value_0.01 %>% arrange(match(gene, pheatmap_ordering_q_value_0.01))
write.table(transcription_factors_table_q_value_0.01, file.path(tables_directory, "5-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6_11-significant_transcription_factors_diff_test_analysis_qval_0.01.txt"), sep="\t", quote=FALSE, row.names=FALSE)
heatmap_matrix_q_value_0.01 <- plot_genes_heatmap_output_q_value_0.01[[1]]
heatmap_matrix_q_value_0.01 <- as.data.frame(heatmap_matrix_q_value_0.01) %>% rownames_to_column("gene")
heatmap_matrix_q_value_0.01 <- heatmap_matrix_q_value_0.01 %>% arrange(match(gene, pheatmap_ordering_q_value_0.01))
heatmap_matrix_q_value_0.01 %>% head(20) %>% kable() %>% kable_styling() %>% scroll_box(height="200px", width="600px")
| gene | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | 32 | 33 | 34 | 35 | 36 | 37 | 38 | 39 | 40 | 41 | 42 | 43 | 44 | 45 | 46 | 47 | 48 | 49 | 50 | 51 | 52 | 53 | 54 | 55 | 56 | 57 | 58 | 59 | 60 | 61 | 62 | 63 | 64 | 65 | 66 | 67 | 68 | 69 | 70 | 71 | 72 | 73 | 74 | 75 | 76 | 77 | 78 | 79 | 80 | 81 | 82 | 83 | 84 | 85 | 86 | 87 | 88 | 89 | 90 | 91 | 92 | 93 | 94 | 95 | 96 | 97 | 98 | 99 | 100 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Thra | 0.0809763 | 0.1142869 | 0.1475813 | 0.1808113 | 0.2139285 | 0.2468843 | 0.2796298 | 0.3121161 | 0.3442939 | 0.3761141 | 0.4075270 | 0.4384831 | 0.4689325 | 0.4988254 | 0.5281115 | 0.5567408 | 0.5846629 | 0.6118274 | 0.6381837 | 0.6636812 | 0.6882693 | 0.7118971 | 0.7345138 | 0.7560687 | 0.7765107 | 0.7957891 | 0.8138530 | 0.8306514 | 0.8461337 | 0.8602490 | 0.8729467 | 0.8841761 | 0.8938869 | 0.9020286 | 0.9085512 | 0.9134045 | 0.9165388 | 0.9179046 | 0.9174524 | 0.9151333 | 0.9108985 | 0.9046994 | 0.8964881 | 0.8862167 | 0.8738381 | 0.8593052 | 0.8425716 | 0.8235914 | 0.8023192 | 0.7787101 | 0.7527217 | 0.7243532 | 0.6936439 | 0.6606345 | 0.6253665 | 0.5878815 | 0.5482214 | 0.5064283 | 0.4625446 | 0.4166130 | 0.3686763 | 0.3187776 | 0.2669599 | 0.2132666 | 0.1577411 | 0.1004269 | 0.0413676 | -0.0193930 | -0.0818114 | -0.1458437 | -0.2114463 | -0.2785753 | -0.3471871 | -0.4172380 | -0.4886845 | -0.5614829 | -0.6355898 | -0.7109620 | -0.7875561 | -0.8653291 | -0.9442382 | -1.0242404 | -1.1052932 | -1.1873543 | -1.2703814 | -1.3543325 | -1.4391660 | -1.5248395 | -1.6112885 | -1.6984223 | -1.7861496 | -1.8743802 | -1.9630245 | -2.0519940 | -2.1412011 | -2.2305591 | -2.3199823 | -2.4093860 | -2.4986864 | -2.5878008 |
| Zfp706 | -0.0765897 | -0.0367229 | 0.0031568 | 0.0429950 | 0.0827369 | 0.1223276 | 0.1617117 | 0.2008333 | 0.2396363 | 0.2780644 | 0.3160609 | 0.3535686 | 0.3905303 | 0.4268884 | 0.4625849 | 0.4975617 | 0.5317605 | 0.5651226 | 0.5975893 | 0.6291017 | 0.6596006 | 0.6890267 | 0.7173207 | 0.7444232 | 0.7702746 | 0.7948153 | 0.8179860 | 0.8397269 | 0.8599787 | 0.8786819 | 0.8957773 | 0.9112057 | 0.9249083 | 0.9368263 | 0.9469012 | 0.9550749 | 0.9612896 | 0.9654879 | 0.9676127 | 0.9676074 | 0.9654160 | 0.9609831 | 0.9542536 | 0.9451735 | 0.9336891 | 0.9197476 | 0.9032970 | 0.8842863 | 0.8626651 | 0.8383843 | 0.8113982 | 0.7817161 | 0.7494001 | 0.7145148 | 0.6771253 | 0.6372972 | 0.5950965 | 0.5505898 | 0.5038436 | 0.4549249 | 0.4039011 | 0.3508394 | 0.2958074 | 0.2388727 | 0.1801030 | 0.1195658 | 0.0573289 | -0.0065404 | -0.0719745 | -0.1389063 | -0.2072688 | -0.2769951 | -0.3480188 | -0.4202737 | -0.4936939 | -0.5682139 | -0.6437688 | -0.7202938 | -0.7977250 | -0.8759986 | -0.9550516 | -1.0348215 | -1.1152463 | -1.1962648 | -1.2778162 | -1.3598406 | -1.4422786 | -1.5250717 | -1.6081603 | -1.6914843 | -1.7749841 | -1.8586009 | -1.9422770 | -2.0259553 | -2.1095796 | -2.1930948 | -2.2764465 | -2.3595812 | -2.4424465 | -2.5249907 |
| Zfp760 | 1.1988863 | 1.1871660 | 1.1754425 | 1.1636969 | 1.1519101 | 1.1400631 | 1.1281373 | 1.1161138 | 1.1039743 | 1.0917001 | 1.0792730 | 1.0666747 | 1.0538872 | 1.0408924 | 1.0276726 | 1.0142101 | 1.0004873 | 0.9864867 | 0.9721912 | 0.9575837 | 0.9426472 | 0.9273649 | 0.9117203 | 0.8956970 | 0.8792789 | 0.8624499 | 0.8451942 | 0.8274964 | 0.8093410 | 0.7907131 | 0.7715978 | 0.7519805 | 0.7318469 | 0.7111831 | 0.6899752 | 0.6682099 | 0.6458741 | 0.6229550 | 0.5994401 | 0.5753174 | 0.5505750 | 0.5252017 | 0.4991864 | 0.4725185 | 0.4451880 | 0.4171849 | 0.3884999 | 0.3591243 | 0.3290494 | 0.2982674 | 0.2667706 | 0.2345494 | 0.2015924 | 0.1678887 | 0.1334280 | 0.0982006 | 0.0621974 | 0.0254103 | -0.0121685 | -0.0505459 | -0.0897281 | -0.1297207 | -0.1705283 | -0.2121551 | -0.2546041 | -0.2978778 | -0.3419779 | -0.3869051 | -0.4326594 | -0.4792400 | -0.5266452 | -0.5748725 | -0.6239184 | -0.6737786 | -0.7244480 | -0.7759206 | -0.8281894 | -0.8812465 | -0.9350834 | -0.9896903 | -1.0450568 | -1.1011715 | -1.1580221 | -1.2155953 | -1.2738771 | -1.3328527 | -1.3925060 | -1.4528189 | -1.5137195 | -1.5750770 | -1.6367613 | -1.6986471 | -1.7606136 | -1.8225447 | -1.8843290 | -1.9458598 | -2.0070354 | -2.0677582 | -2.1279357 | -2.1874796 |
| Id1 | 1.4871422 | 1.4381725 | 1.3894833 | 1.3411226 | 1.2931377 | 1.2455749 | 1.1984795 | 1.1518958 | 1.1058674 | 1.0604368 | 1.0156456 | 0.9715347 | 0.9281439 | 0.8855122 | 0.8436780 | 0.8026786 | 0.7625507 | 0.7233304 | 0.6850529 | 0.6477527 | 0.6114640 | 0.5762202 | 0.5420543 | 0.5089987 | 0.4770855 | 0.4463464 | 0.4168129 | 0.3885160 | 0.3614870 | 0.3357566 | 0.3113557 | 0.2883152 | 0.2666661 | 0.2464396 | 0.2276672 | 0.2103805 | 0.1946119 | 0.1803940 | 0.1677600 | 0.1567441 | 0.1473808 | 0.1397059 | 0.1337558 | 0.1295683 | 0.1271821 | 0.1266372 | 0.1279752 | 0.1312388 | 0.1364727 | 0.1437230 | 0.1530277 | 0.1642137 | 0.1769041 | 0.1907122 | 0.2052487 | 0.2201220 | 0.2349368 | 0.2492952 | 0.2627959 | 0.2750354 | 0.2856078 | 0.2941061 | 0.3001230 | 0.3032521 | 0.3030896 | 0.2992353 | 0.2912950 | 0.2788825 | 0.2616214 | 0.2391483 | 0.2111148 | 0.1771908 | 0.1370677 | 0.0904614 | 0.0371163 | -0.0231912 | -0.0906488 | -0.1654039 | -0.2475593 | -0.3371692 | -0.4342341 | -0.5386972 | -0.6504391 | -0.7692745 | -0.8949478 | -1.0271304 | -1.1654176 | -1.3093116 | -1.4577780 | -1.6092531 | -1.7622270 | -1.9152926 | -2.0671595 | -2.2166656 | -2.3627842 | -2.5046291 | -2.6414553 | -2.7726568 | -2.8977616 | -3.0000000 |
| Msx2 | 1.2595102 | 1.2236724 | 1.1881777 | 1.1530591 | 1.1183487 | 1.0840771 | 1.0502741 | 1.0169680 | 0.9841864 | 0.9519556 | 0.9203010 | 0.8892473 | 0.8588179 | 0.8290356 | 0.7999225 | 0.7714997 | 0.7437877 | 0.7168065 | 0.6905755 | 0.6651133 | 0.6404384 | 0.6165687 | 0.5935217 | 0.5713147 | 0.5499647 | 0.5294887 | 0.5099033 | 0.4912253 | 0.4734715 | 0.4566586 | 0.4408036 | 0.4259237 | 0.4120364 | 0.3991596 | 0.3873115 | 0.3765109 | 0.3667772 | 0.3581305 | 0.3505915 | 0.3441820 | 0.3389245 | 0.3348426 | 0.3319609 | 0.3303056 | 0.3299037 | 0.3307839 | 0.3329766 | 0.3365135 | 0.3414283 | 0.3477566 | 0.3555239 | 0.3644971 | 0.3741921 | 0.3841093 | 0.3937433 | 0.4025829 | 0.4101117 | 0.4158099 | 0.4191568 | 0.4196341 | 0.4167297 | 0.4099428 | 0.3987892 | 0.3828077 | 0.3615669 | 0.3346723 | 0.3017738 | 0.2625735 | 0.2168333 | 0.1643824 | 0.1051237 | 0.0390406 | -0.0337983 | -0.1132353 | -0.1990211 | -0.2908140 | -0.3881817 | -0.4906037 | -0.5974778 | -0.7081267 | -0.8218084 | -0.9377277 | -1.0550496 | -1.1729142 | -1.2904527 | -1.4068041 | -1.5211318 | -1.6326299 | -1.7402677 | -1.8428948 | -1.9396463 | -2.0299386 | -2.1134371 | -2.1900192 | -2.2597371 | -2.3227815 | -2.3794476 | -2.4301048 | -2.4751708 | -2.5150894 |
| Pitx3 | -0.4367448 | -0.4044712 | -0.3631641 | -0.3106588 | -0.2444708 | -0.1618466 | -0.0598691 | 0.0643629 | 0.2134704 | 0.3894350 | 0.5931541 | 0.8239338 | 1.0789679 | 1.3528796 | 1.6374201 | 1.9214327 | 2.1911818 | 2.4311121 | 2.6250464 | 2.7577470 | 2.8166765 | 2.7937163 | 2.6865517 | 2.4994409 | 2.2431577 | 1.9340245 | 1.5921304 | 1.2389970 | 0.8950870 | 0.5775932 | 0.2988844 | 0.0658297 | -0.1199800 | -0.2612864 | -0.3637950 | -0.4347155 | -0.4814913 | -0.5108860 | -0.5284743 | -0.5384872 | -0.5439060 | -0.5466913 | -0.5480499 | -0.5486780 | -0.5489530 | -0.5490669 | -0.5491115 | -0.5491280 | -0.5491337 | -0.5491356 | -0.5491362 | -0.5491363 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491364 | -0.5491363 | -0.5491356 | -0.5491155 | -0.5485856 | -0.5340411 | -0.1280237 |
| Jun | -0.2299473 | -0.1659870 | -0.1019971 | -0.0380964 | 0.0255949 | 0.0889557 | 0.1518637 | 0.2141958 | 0.2758280 | 0.3366353 | 0.3964919 | 0.4552710 | 0.5128454 | 0.5690868 | 0.6238666 | 0.6770553 | 0.7285232 | 0.7781400 | 0.8257749 | 0.8712971 | 0.9145753 | 0.9554783 | 0.9938747 | 1.0296333 | 1.0626229 | 1.0927126 | 1.1197720 | 1.1436709 | 1.1642799 | 1.1814701 | 1.1951135 | 1.2050831 | 1.2112529 | 1.2134980 | 1.2116949 | 1.2057218 | 1.1954582 | 1.1807857 | 1.1615875 | 1.1377494 | 1.1091593 | 1.0757074 | 1.0372871 | 0.9937943 | 0.9451284 | 0.8911918 | 0.8318909 | 0.7671358 | 0.6968407 | 0.6209245 | 0.5393272 | 0.4523487 | 0.3606283 | 0.2648146 | 0.1655514 | 0.0634760 | -0.0407812 | -0.1465971 | -0.2533571 | -0.3604552 | -0.4672942 | -0.5732864 | -0.6778533 | -0.7804258 | -0.8804439 | -0.9773565 | -1.0706207 | -1.1597015 | -1.2440709 | -1.3232071 | -1.3965930 | -1.4637155 | -1.5240640 | -1.5771286 | -1.6223985 | -1.6593604 | -1.6874962 | -1.7062809 | -1.7151807 | -1.7136502 | -1.7011299 | -1.6770438 | -1.6407968 | -1.5917715 | -1.5293256 | -1.4527894 | -1.3614621 | -1.2546354 | -1.1323688 | -0.9956466 | -0.8455124 | -0.6830225 | -0.5092526 | -0.3253024 | -0.1323006 | 0.0685918 | 0.2761784 | 0.4892262 | 0.7064635 | 0.9265802 |
| Lmx1a | 0.4676597 | 0.5002755 | 0.5331323 | 0.5661477 | 0.5992363 | 0.6323092 | 0.6652744 | 0.6980363 | 0.7304966 | 0.7625533 | 0.7941017 | 0.8250340 | 0.8552397 | 0.8846057 | 0.9130165 | 0.9403547 | 0.9665007 | 0.9913338 | 1.0147320 | 1.0365725 | 1.0567323 | 1.0750885 | 1.0915188 | 1.1059020 | 1.1181188 | 1.1280519 | 1.1355873 | 1.1406140 | 1.1430254 | 1.1427198 | 1.1396008 | 1.1335781 | 1.1245684 | 1.1124957 | 1.0972922 | 1.0788989 | 1.0572662 | 1.0323545 | 1.0041346 | 0.9725887 | 0.9377103 | 0.8995049 | 0.8579906 | 0.8131977 | 0.7651697 | 0.7139631 | 0.6596472 | 0.6023048 | 0.5420313 | 0.4789350 | 0.4131449 | 0.3449714 | 0.2748797 | 0.2033206 | 0.1307214 | 0.0574839 | -0.0160165 | -0.0894320 | -0.1624422 | -0.2347543 | -0.3061029 | -0.3762490 | -0.4449794 | -0.5121054 | -0.5774614 | -0.6409037 | -0.7023090 | -0.7615725 | -0.8186066 | -0.8733389 | -0.9257109 | -0.9756762 | -1.0231988 | -1.0682514 | -1.1108143 | -1.1508734 | -1.1884190 | -1.2234445 | -1.2559446 | -1.2859143 | -1.3133475 | -1.3382357 | -1.3605665 | -1.3803226 | -1.3974804 | -1.4120082 | -1.4238652 | -1.4330045 | -1.4395131 | -1.4436328 | -1.4455994 | -1.4456364 | -1.4439587 | -1.4407747 | -1.4362896 | -1.4307073 | -1.4242321 | -1.4170701 | -1.4094312 | -1.4015289 |
| Smad6 | 0.0598186 | 0.1088869 | 0.1587385 | 0.2092800 | 0.2604107 | 0.3120222 | 0.3639986 | 0.4162159 | 0.4685423 | 0.5208379 | 0.5729549 | 0.6247374 | 0.6760218 | 0.7266370 | 0.7764047 | 0.8251395 | 0.8726499 | 0.9187384 | 0.9632023 | 1.0058345 | 1.0464244 | 1.0847587 | 1.1206224 | 1.1538001 | 1.1840772 | 1.2112410 | 1.2350822 | 1.2553966 | 1.2719861 | 1.2846606 | 1.2932397 | 1.2975538 | 1.2974465 | 1.2927755 | 1.2834147 | 1.2692556 | 1.2502085 | 1.2262046 | 1.1971966 | 1.1631605 | 1.1240961 | 1.0800283 | 1.0310075 | 0.9771106 | 0.9184406 | 0.8551272 | 0.7873264 | 0.7152200 | 0.6390153 | 0.5589435 | 0.4752726 | 0.3885714 | 0.2996545 | 0.2092960 | 0.1182133 | 0.0270635 | -0.0635575 | -0.1531159 | -0.2411387 | -0.3272122 | -0.4109790 | -0.4921352 | -0.5704263 | -0.6456433 | -0.7176184 | -0.7862206 | -0.8513512 | -0.9129393 | -0.9709378 | -1.0253189 | -1.0760704 | -1.1231915 | -1.1666894 | -1.2065760 | -1.2428639 | -1.2755637 | -1.3046809 | -1.3302123 | -1.3521434 | -1.3704447 | -1.3850687 | -1.3959461 | -1.4029820 | -1.4060512 | -1.4049936 | -1.3996082 | -1.3896463 | -1.3748122 | -1.3550099 | -1.3304038 | -1.3011494 | -1.2673872 | -1.2292523 | -1.1868844 | -1.1404374 | -1.0900892 | -1.0360511 | -0.9785771 | -0.9179740 | -0.8546094 |
| Klf10 | -0.0366176 | 0.0157093 | 0.0685285 | 0.1217438 | 0.1752548 | 0.2289564 | 0.2827391 | 0.3364886 | 0.3900865 | 0.4434095 | 0.4963302 | 0.5487166 | 0.6004328 | 0.6513385 | 0.7012900 | 0.7501396 | 0.7977363 | 0.8439263 | 0.8885528 | 0.9314568 | 0.9724773 | 1.0114518 | 1.0482168 | 1.0826084 | 1.1144627 | 1.1436165 | 1.1699077 | 1.1931765 | 1.2132655 | 1.2300205 | 1.2432918 | 1.2529343 | 1.2588084 | 1.2607812 | 1.2587267 | 1.2525273 | 1.2420739 | 1.2272672 | 1.2080184 | 1.1842497 | 1.1558954 | 1.1229027 | 1.0852318 | 1.0428572 | 0.9957681 | 0.9439688 | 0.8874793 | 0.8263359 | 0.7605910 | 0.6903142 | 0.6156043 | 0.5368436 | 0.4546648 | 0.3696913 | 0.2825231 | 0.1937338 | 0.1038689 | 0.0134436 | -0.0770575 | -0.1671815 | -0.2565071 | -0.3446443 | -0.4312334 | -0.5159445 | -0.5984758 | -0.6785521 | -0.7559229 | -0.8303608 | -0.9016590 | -0.9696292 | -1.0340994 | -1.0949113 | -1.1519179 | -1.2049810 | -1.2539685 | -1.2987516 | -1.3392026 | -1.3751915 | -1.4065834 | -1.4332356 | -1.4549941 | -1.4716905 | -1.4831384 | -1.4891297 | -1.4894301 | -1.4837750 | -1.4718640 | -1.4533672 | -1.4282666 | -1.3969295 | -1.3597295 | -1.3170317 | -1.2692009 | -1.2166094 | -1.1596445 | -1.0987150 | -1.0342575 | -0.9667421 | -0.8966775 | -0.8246155 |
| Ets1 | 1.8481815 | 1.8067570 | 1.7656250 | 1.7247655 | 1.6841594 | 1.6437877 | 1.6036321 | 1.5636750 | 1.5238990 | 1.4842876 | 1.4448244 | 1.4054937 | 1.3662805 | 1.3271700 | 1.2881481 | 1.2492009 | 1.2103154 | 1.1714788 | 1.1326788 | 1.0939037 | 1.0551422 | 1.0163836 | 0.9776175 | 0.9388340 | 0.9000239 | 0.8611783 | 0.8222887 | 0.7833473 | 0.7443465 | 0.7052795 | 0.6661397 | 0.6269211 | 0.5876182 | 0.5482259 | 0.5087397 | 0.4691554 | 0.4294694 | 0.3896786 | 0.3497802 | 0.3097721 | 0.2696525 | 0.2294201 | 0.1890742 | 0.1486145 | 0.1080410 | 0.0673544 | 0.0265557 | -0.0143535 | -0.0553713 | -0.0964953 | -0.1377205 | -0.1789994 | -0.2202461 | -0.2613768 | -0.3023113 | -0.3429731 | -0.3832895 | -0.4231913 | -0.4626127 | -0.5014915 | -0.5397685 | -0.5773881 | -0.6142972 | -0.6504462 | -0.6857877 | -0.7202773 | -0.7538729 | -0.7865345 | -0.8182246 | -0.8489072 | -0.8785483 | -0.9071153 | -0.9345771 | -0.9609035 | -0.9860657 | -1.0100353 | -1.0327845 | -1.0542862 | -1.0745130 | -1.0934378 | -1.1110329 | -1.1272705 | -1.1421218 | -1.1555570 | -1.1675453 | -1.1780543 | -1.1870500 | -1.1944988 | -1.2004425 | -1.2050110 | -1.2083355 | -1.2105447 | -1.2117650 | -1.2121214 | -1.2117376 | -1.2107366 | -1.2092412 | -1.2073741 | -1.2052581 | -1.2030164 |
| Mta3 | 1.9442808 | 1.8952440 | 1.8464660 | 1.7979498 | 1.7496986 | 1.7017151 | 1.6540022 | 1.6065628 | 1.5593993 | 1.5125144 | 1.4659107 | 1.4195905 | 1.3735563 | 1.3278102 | 1.2823545 | 1.2371914 | 1.1923228 | 1.1477509 | 1.1034774 | 1.0595043 | 1.0158333 | 0.9724662 | 0.9294046 | 0.8866501 | 0.8442043 | 0.8020686 | 0.7602444 | 0.7187330 | 0.6775359 | 0.6366541 | 0.5960890 | 0.5558416 | 0.5159129 | 0.4763041 | 0.4370161 | 0.3980499 | 0.3594062 | 0.3210860 | 0.2830901 | 0.2454191 | 0.2080738 | 0.1710548 | 0.1343628 | 0.0979983 | 0.0619619 | 0.0262541 | -0.0091246 | -0.0441738 | -0.0788932 | -0.1132823 | -0.1473408 | -0.1810699 | -0.2144716 | -0.2475483 | -0.2803021 | -0.3127354 | -0.3448502 | -0.3766488 | -0.4081334 | -0.4393060 | -0.4701687 | -0.5007237 | -0.5309731 | -0.5609188 | -0.5905630 | -0.6199077 | -0.6489548 | -0.6777063 | -0.7061642 | -0.7343304 | -0.7622069 | -0.7897956 | -0.8170983 | -0.8441168 | -0.8708532 | -0.8973091 | -0.9234863 | -0.9493868 | -0.9750121 | -1.0003642 | -1.0254447 | -1.0502553 | -1.0747977 | -1.0990736 | -1.1230846 | -1.1468325 | -1.1703188 | -1.1935452 | -1.2165200 | -1.2392583 | -1.2617757 | -1.2840874 | -1.3062085 | -1.3281537 | -1.3499378 | -1.3715750 | -1.3930796 | -1.4144655 | -1.4357467 | -1.4569366 |
| E2f5 | 1.8562881 | 1.8165953 | 1.7770033 | 1.7375020 | 1.6980815 | 1.6587318 | 1.6194432 | 1.5802061 | 1.5410110 | 1.5018485 | 1.4627093 | 1.4235841 | 1.3844639 | 1.3453398 | 1.3062028 | 1.2670443 | 1.2278557 | 1.1886283 | 1.1493538 | 1.1100239 | 1.0706305 | 1.0311655 | 0.9916209 | 0.9519890 | 0.9122619 | 0.8724322 | 0.8324924 | 0.7924352 | 0.7522532 | 0.7119395 | 0.6714870 | 0.6308889 | 0.5901386 | 0.5492293 | 0.5081546 | 0.4669083 | 0.4254841 | 0.3838760 | 0.3420780 | 0.3000843 | 0.2578893 | 0.2154875 | 0.1728735 | 0.1300422 | 0.0869883 | 0.0437070 | 0.0001935 | -0.0435568 | -0.0875485 | -0.1317858 | -0.1762703 | -0.2209488 | -0.2657165 | -0.3104682 | -0.3551003 | -0.3995109 | -0.4435996 | -0.4872679 | -0.5304185 | -0.5729561 | -0.6147865 | -0.6558172 | -0.6959571 | -0.7351162 | -0.7732060 | -0.8101390 | -0.8458288 | -0.8801898 | -0.9131376 | -0.9445882 | -0.9744582 | -1.0026648 | -1.0291255 | -1.0537578 | -1.0764793 | -1.0972076 | -1.1158596 | -1.1323520 | -1.1466005 | -1.1585203 | -1.1680249 | -1.1750271 | -1.1794375 | -1.1811654 | -1.1801177 | -1.1761992 | -1.1693121 | -1.1593605 | -1.1463978 | -1.1306536 | -1.1123665 | -1.0917752 | -1.0691186 | -1.0446365 | -1.0185701 | -0.9911624 | -0.9626587 | -0.9333065 | -0.9033562 | -0.8730609 |
| Dmrtb1 | 1.8338638 | 1.8052919 | 1.7768570 | 1.7484327 | 1.7198971 | 1.6911332 | 1.6620292 | 1.6324782 | 1.6023785 | 1.5716339 | 1.5401538 | 1.5078536 | 1.4746549 | 1.4404857 | 1.4052808 | 1.3689824 | 1.3315400 | 1.2929108 | 1.2530605 | 1.2119629 | 1.1696008 | 1.1259658 | 1.0810587 | 1.0348900 | 0.9874794 | 0.9388566 | 0.8890605 | 0.8381400 | 0.7861533 | 0.7331680 | 0.6792608 | 0.6245169 | 0.5690301 | 0.5129017 | 0.4562402 | 0.3991606 | 0.3417838 | 0.2842354 | 0.2266451 | 0.1691456 | 0.1118716 | 0.0549589 | -0.0014569 | -0.0572412 | -0.1122619 | -0.1663903 | -0.2195019 | -0.2714779 | -0.3222059 | -0.3715807 | -0.4195004 | -0.4657708 | -0.5101448 | -0.5524332 | -0.5925035 | -0.6302734 | -0.6657041 | -0.6987939 | -0.7295719 | -0.7580921 | -0.7844279 | -0.8086673 | -0.8309087 | -0.8512568 | -0.8698202 | -0.8867076 | -0.9020269 | -0.9158826 | -0.9283745 | -0.9395971 | -0.9496383 | -0.9585791 | -0.9664929 | -0.9734455 | -0.9794944 | -0.9846890 | -0.9890700 | -0.9926693 | -0.9955094 | -0.9976030 | -0.9989523 | -0.9995478 | -0.9993670 | -0.9983729 | -0.9965112 | -0.9937076 | -0.9898639 | -0.9848543 | -0.9785746 | -0.9709596 | -0.9619291 | -0.9513872 | -0.9392244 | -0.9253208 | -0.9095493 | -0.8917805 | -0.8718879 | -0.8497554 | -0.8252851 | -0.7984082 |
| Klf5 | 1.1740817 | 1.1729262 | 1.1717193 | 1.1704091 | 1.1689442 | 1.1672728 | 1.1653435 | 1.1631050 | 1.1605061 | 1.1574957 | 1.1540231 | 1.1500378 | 1.1454895 | 1.1403285 | 1.1345054 | 1.1279715 | 1.1206784 | 1.1125785 | 1.1036252 | 1.0937722 | 1.0829748 | 1.0711886 | 1.0583709 | 1.0444799 | 1.0294753 | 1.0133180 | 0.9959707 | 0.9773977 | 0.9575648 | 0.9364400 | 0.9139932 | 0.8901963 | 0.8650236 | 0.8384515 | 0.8104590 | 0.7810276 | 0.7501416 | 0.7177877 | 0.6839559 | 0.6486387 | 0.6118321 | 0.5735347 | 0.5337488 | 0.4924796 | 0.4497358 | 0.4055293 | 0.3598756 | 0.3127934 | 0.2643052 | 0.2144365 | 0.1632210 | 0.1107867 | 0.0573454 | 0.0031046 | -0.0517363 | -0.1069867 | -0.1624651 | -0.2179991 | -0.2734255 | -0.3285905 | -0.3833496 | -0.4375673 | -0.4911171 | -0.5438811 | -0.5957501 | -0.6466228 | -0.6964055 | -0.7450122 | -0.7923635 | -0.8383866 | -0.8830148 | -0.9261867 | -0.9678461 | -1.0079414 | -1.0464249 | -1.0832526 | -1.1183833 | -1.1517785 | -1.1834015 | -1.2132172 | -1.2411913 | -1.2672901 | -1.2914796 | -1.3137250 | -1.3339905 | -1.3522384 | -1.3684285 | -1.3825213 | -1.3945828 | -1.4048006 | -1.4133611 | -1.4204443 | -1.4262248 | -1.4308726 | -1.4345544 | -1.4374344 | -1.4396748 | -1.4414364 | -1.4428792 | -1.4441624 |
| Maf | 1.4928511 | 1.4743189 | 1.4557993 | 1.4372581 | 1.4186615 | 1.3999763 | 1.3811693 | 1.3622079 | 1.3430599 | 1.3236932 | 1.3040763 | 1.2841781 | 1.2639677 | 1.2434150 | 1.2224899 | 1.2011631 | 1.1794055 | 1.1571887 | 1.1344847 | 1.1112659 | 1.0875056 | 1.0631773 | 1.0382553 | 1.0127145 | 0.9865304 | 0.9596792 | 0.9321377 | 0.9038836 | 0.8748953 | 0.8451518 | 0.8146332 | 0.7833202 | 0.7511946 | 0.7182389 | 0.6844365 | 0.6497721 | 0.6142310 | 0.5777996 | 0.5404657 | 0.5022176 | 0.4630453 | 0.4229394 | 0.3818922 | 0.3398966 | 0.2969473 | 0.2530398 | 0.2081711 | 0.1623395 | 0.1155444 | 0.0677866 | 0.0190724 | -0.0305089 | -0.0807915 | -0.1316113 | -0.1828089 | -0.2342298 | -0.2857249 | -0.3371498 | -0.3883657 | -0.4392386 | -0.4896396 | -0.5394448 | -0.5885352 | -0.6367963 | -0.6841183 | -0.7303955 | -0.7755264 | -0.8194133 | -0.8619620 | -0.9030815 | -0.9426838 | -0.9806837 | -1.0169981 | -1.0515458 | -1.0842472 | -1.1150241 | -1.1437988 | -1.1704940 | -1.1950326 | -1.2173366 | -1.2373272 | -1.2549243 | -1.2700456 | -1.2826062 | -1.2925186 | -1.2996910 | -1.3040280 | -1.3054337 | -1.3039610 | -1.2998379 | -1.2932981 | -1.2845727 | -1.2738912 | -1.2614826 | -1.2475764 | -1.2324034 | -1.2161965 | -1.1991914 | -1.1816270 | -1.1637456 |
| Mafb | 1.4075855 | 1.3983572 | 1.3890850 | 1.3797053 | 1.3701554 | 1.3603731 | 1.3502966 | 1.3398650 | 1.3290180 | 1.3176962 | 1.3058409 | 1.2933942 | 1.2802995 | 1.2665010 | 1.2519443 | 1.2365760 | 1.2203443 | 1.2031989 | 1.1850910 | 1.1659736 | 1.1458017 | 1.1245322 | 1.1021242 | 1.0785391 | 1.0537407 | 1.0276955 | 1.0003727 | 0.9717444 | 0.9417856 | 0.9104747 | 0.8777931 | 0.8437259 | 0.8082617 | 0.7713927 | 0.7331151 | 0.6934286 | 0.6523374 | 0.6098493 | 0.5659766 | 0.5207357 | 0.4741471 | 0.4262358 | 0.3770308 | 0.3265657 | 0.2748781 | 0.2220098 | 0.1680071 | 0.1129198 | 0.0568022 | -0.0002880 | -0.0582827 | -0.1169799 | -0.1760635 | -0.2352331 | -0.2942098 | -0.3527360 | -0.4105758 | -0.4675137 | -0.5233549 | -0.5779235 | -0.6310625 | -0.6826320 | -0.7325082 | -0.7805822 | -0.8267586 | -0.8709540 | -0.9130960 | -0.9531212 | -0.9909743 | -1.0266064 | -1.0599737 | -1.0910359 | -1.1197553 | -1.1460946 | -1.1700164 | -1.1914810 | -1.2104457 | -1.2268625 | -1.2406773 | -1.2518279 | -1.2602424 | -1.2658372 | -1.2685155 | -1.2681644 | -1.2646531 | -1.2578299 | -1.2475191 | -1.2335241 | -1.2158079 | -1.1945361 | -1.1698771 | -1.1419959 | -1.1110582 | -1.0772361 | -1.0407122 | -1.0016845 | -0.9603701 | -0.9170097 | -0.8718711 | -0.8252529 |
| Zfp180 | 1.6338540 | 1.6091382 | 1.5844952 | 1.5598835 | 1.5352622 | 1.5105914 | 1.4858319 | 1.4609452 | 1.4358938 | 1.4106407 | 1.3851499 | 1.3593864 | 1.3333157 | 1.3069043 | 1.2801199 | 1.2529306 | 1.2253058 | 1.1972159 | 1.1686320 | 1.1395267 | 1.1098733 | 1.0796464 | 1.0488217 | 1.0173761 | 0.9852876 | 0.9525357 | 0.9191011 | 0.8849658 | 0.8501131 | 0.8145280 | 0.7781967 | 0.7411070 | 0.7032482 | 0.6646113 | 0.6251886 | 0.5849744 | 0.5439644 | 0.5021561 | 0.4595487 | 0.4161432 | 0.3719422 | 0.3269504 | 0.2811739 | 0.2346209 | 0.1873014 | 0.1392271 | 0.0904115 | 0.0408702 | -0.0093799 | -0.0603195 | -0.1119232 | -0.1640642 | -0.2165263 | -0.2691002 | -0.3215875 | -0.3738011 | -0.4255648 | -0.4767132 | -0.5270914 | -0.5765550 | -0.6249691 | -0.6722083 | -0.7181560 | -0.7627038 | -0.8057509 | -0.8472034 | -0.8869739 | -0.9249801 | -0.9611449 | -0.9953951 | -1.0276606 | -1.0578741 | -1.0859695 | -1.1118820 | -1.1355463 | -1.1568965 | -1.1758647 | -1.1923802 | -1.2063686 | -1.2177506 | -1.2264410 | -1.2323476 | -1.2353699 | -1.2353975 | -1.2323093 | -1.2259713 | -1.2162352 | -1.2029422 | -1.1860980 | -1.1659102 | -1.1425932 | -1.1163598 | -1.0874247 | -1.0560069 | -1.0223328 | -0.9866389 | -0.9491734 | -0.9101992 | -0.8699950 | -0.8288571 |
| Rbck1 | 1.0897522 | 1.0951413 | 1.1004646 | 1.1056533 | 1.1106387 | 1.1153518 | 1.1197236 | 1.1236849 | 1.1271667 | 1.1300996 | 1.1324145 | 1.1340423 | 1.1349137 | 1.1349600 | 1.1341123 | 1.1323020 | 1.1294610 | 1.1255213 | 1.1204154 | 1.1140764 | 1.1064378 | 1.0974339 | 1.0869997 | 1.0750710 | 1.0615843 | 1.0464776 | 1.0296895 | 1.0111601 | 0.9908307 | 0.9686440 | 0.9445444 | 0.9184776 | 0.8903914 | 0.8602353 | 0.8279608 | 0.7935214 | 0.7568731 | 0.7179739 | 0.6767846 | 0.6332683 | 0.5873911 | 0.5391217 | 0.4884317 | 0.4352961 | 0.3796927 | 0.3216028 | 0.2610112 | 0.1979061 | 0.1322791 | 0.0641260 | -0.0065435 | -0.0794923 | -0.1542746 | -0.2304475 | -0.3075799 | -0.3852534 | -0.4630627 | -0.5406159 | -0.6175341 | -0.6934518 | -0.7680160 | -0.8408865 | -0.9117346 | -0.9802426 | -1.0461032 | -1.1090182 | -1.1686975 | -1.2248578 | -1.2772217 | -1.3255155 | -1.3694685 | -1.4088108 | -1.4432716 | -1.4725776 | -1.4964509 | -1.5146068 | -1.5267514 | -1.5325796 | -1.5317723 | -1.5239934 | -1.5088875 | -1.4860760 | -1.4551541 | -1.4156868 | -1.3672050 | -1.3092013 | -1.2411248 | -1.1623924 | -1.0728922 | -0.9730990 | -0.8635232 | -0.7446851 | -0.6171227 | -0.4813996 | -0.3381121 | -0.1878959 | -0.0314327 | 0.1305444 | 0.2972455 | 0.4678195 |
| Smarca1 | 0.9527755 | 0.9684955 | 0.9841820 | 0.9997492 | 1.0151098 | 1.0301758 | 1.0448581 | 1.0590665 | 1.0727101 | 1.0856972 | 1.0979353 | 1.1093316 | 1.1197926 | 1.1292248 | 1.1375346 | 1.1446285 | 1.1504133 | 1.1547965 | 1.1576864 | 1.1589923 | 1.1586249 | 1.1564965 | 1.1525215 | 1.1466162 | 1.1386999 | 1.1286945 | 1.1165252 | 1.1021209 | 1.0854145 | 1.0663430 | 1.0448482 | 1.0208770 | 0.9943817 | 0.9653202 | 0.9336567 | 0.8993618 | 0.8624129 | 0.8227945 | 0.7804986 | 0.7355246 | 0.6878804 | 0.6375815 | 0.5846522 | 0.5291252 | 0.4710421 | 0.4104531 | 0.3474174 | 0.2820030 | 0.2142869 | 0.1443549 | 0.0723116 | -0.0015147 | -0.0766040 | -0.1524567 | -0.2286045 | -0.3046110 | -0.3800722 | -0.4546167 | -0.5279048 | -0.5996277 | -0.6695067 | -0.7372907 | -0.8027554 | -0.8657004 | -0.9259477 | -0.9833390 | -1.0377332 | -1.0890041 | -1.1370379 | -1.1817302 | -1.2229839 | -1.2607058 | -1.2948045 | -1.3251872 | -1.3517571 | -1.3744102 | -1.3930324 | -1.4074960 | -1.4176565 | -1.4233487 | -1.4243824 | -1.4205385 | -1.4115632 | -1.3971630 | -1.3769980 | -1.3506747 | -1.3177376 | -1.2776706 | -1.2302300 | -1.1755357 | -1.1137144 | -1.0448879 | -0.9691855 | -0.8867554 | -0.7977758 | -0.7024675 | -0.6011050 | -0.4940283 | -0.3816547 | -0.2644893 |
write.table(heatmap_matrix_q_value_0.01, file = file.path(tables_directory, "5-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6_11-significant_transcription_factors_diff_test_analysis_qval_0.01_heatmap_matrix.txt"), sep="\t", quote=FALSE, row.names=FALSE)
transcription_factors_table_q_value_5_10_minus_5_ordered_qval <- arrange(transcription_factors_table_q_value_5_10_minus_5, qval)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[1]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[2]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[3]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[4]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[5]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[6]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[7]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[8]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[9]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
marker <- transcription_factors_table_q_value_5_10_minus_5_ordered_qval$gene[10]
p1 <- plot_cell_trajectory(monocle, markers=marker)
p2 <- plot_cell_trajectory(monocle, use_color_gradient = TRUE, markers=marker)
show(p1+p2)
# Genes of interest.
genes_of_interest <- c("Aqp4", "Fabp7", "Kif9", "Mbp", "Nes", "Pdgfra", "Top2a")
# Remove genes of interest not present in Seurat dataset
genes_not_present <- genes_of_interest[!genes_of_interest %in% rownames(seurat@data)]
genes_of_interest <- genes_of_interest[!genes_of_interest %in% genes_not_present]
if(length(genes_not_present != 0)) {
print(paste0("The following genes were not present in the Seurat object", genes_not_present))
}
diff_test_res <- differentialGeneTest(monocle[genes_of_interest],
fullModelFormulaStr = "~sm.ns(Pseudotime)")
sig_gene_names <- row.names(subset(diff_test_res, qval < 0.1))
plot_pseudotime_heatmap(monocle[genes_of_interest,],
num_clusters = 1,
cores = 1,
show_rownames = T)
p <- plot_genes_in_pseudotime(monocle[genes_of_interest,], color_by="cluster") + scale_color_manual(values=colours)
p <- p %>% remove_geom("point")
p <- p %>% remove_geom("Line")
p <- p %>% + geom_line(aes(x = Pseudotime, y = expectation), size=1)
show(p)
p <- plot_genes_branched_pseudotime(monocle[genes_of_interest,], color_by="cluster") + scale_color_manual(values=colours)
show(p)
p <- p %>% remove_geom("point")
show(p)
p <- cytokit::tsne(seurat, label=FALSE)
show(p)
p <- tsne_plot_clusters_highlighted(seurat, selected_clusters, legend=TRUE)
show(p)
p <- p + theme(legend.position = "none")
show(p)
p <- tsne_plot_clusters_highlighted_with_pseudotime(seurat, monocle, selected_clusters, legend=TRUE)
show(p)
p <- p + theme(legend.position = "none")
show(p)
save(monocle, file=file.path(monocle_objects_directory, "5-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6_11.Rda"))
cells_pseudotime <- pData(monocle) %>% select(cell, Pseudotime) %>% rename(pseudotime=Pseudotime)
write.table(cells_pseudotime, file.path(tables_directory, "5-hindbrain_astro_ependymal_joint_pons_clusters_20_13_15_3_6_11_cell_pseudotime.txt"), sep="\t", quote=FALSE, row.names=FALSE)
sessionInfo()
## R version 3.5.0 (2018-04-23)
## Platform: x86_64-redhat-linux-gnu (64-bit)
## Running under: CentOS Linux 7 (Core)
##
## Matrix products: default
## BLAS/LAPACK: /var/chroots/hydraex-centos-7/usr/lib64/R/lib/libRblas.so
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] splines stats4 parallel stats graphics grDevices utils
## [8] datasets methods base
##
## other attached packages:
## [1] viridis_0.5.1 viridisLite_0.3.0 forcats_0.4.0
## [4] stringr_1.4.0 dplyr_0.8.0.1 purrr_0.3.0
## [7] tidyr_0.8.2 tibble_2.0.1 tidyverse_1.2.1
## [10] Seurat_2.3.4 cowplot_0.9.4 R.utils_2.8.0
## [13] R.oo_1.22.0 R.methodsS3_1.7.1 readr_1.3.1
## [16] readxl_1.3.0 patchwork_0.0.1 monocle_2.10.1
## [19] DDRTree_0.1.5 irlba_2.3.3 VGAM_1.1-1
## [22] Biobase_2.42.0 BiocGenerics_0.28.0 Matrix_1.2-15
## [25] kableExtra_1.0.1 ggedit_0.3.0 ggplot2_3.1.0
## [28] cytokit_0.6.0 pheatmap_1.0.12 colorRamps_2.3
##
## loaded via a namespace (and not attached):
## [1] snow_0.4-3 backports_1.1.3 Hmisc_4.2-0
## [4] plyr_1.8.4 igraph_1.2.4 lazyeval_0.2.2
## [7] densityClust_0.3 fastICA_1.2-1 digest_0.6.18
## [10] foreach_1.4.4 htmltools_0.3.6 lars_1.2
## [13] gdata_2.18.0 magrittr_1.5 checkmate_1.9.1
## [16] cluster_2.0.7-1 mixtools_1.1.0 ROCR_1.0-7
## [19] limma_3.38.3 modelr_0.1.3 matrixStats_0.54.0
## [22] docopt_0.6.1 colorspace_1.4-0 ggrepel_0.8.0
## [25] rvest_0.3.2 haven_2.0.0 xfun_0.4
## [28] sparsesvd_0.1-4 crayon_1.3.4 jsonlite_1.6
## [31] survival_2.43-3 zoo_1.8-4 iterators_1.0.10
## [34] ape_5.2 glue_1.3.0 gtable_0.2.0
## [37] webshot_0.5.1 kernlab_0.9-27 prabclus_2.2-7
## [40] DEoptimR_1.0-8 scales_1.0.0 mvtnorm_1.0-8
## [43] bibtex_0.4.2 miniUI_0.1.1.1 Rcpp_1.0.0
## [46] metap_1.1 dtw_1.20-1 xtable_1.8-3
## [49] htmlTable_1.13.1 reticulate_1.11.1 foreign_0.8-71
## [52] bit_1.1-14 proxy_0.4-22 mclust_5.4.2
## [55] SDMTools_1.1-221 Formula_1.2-3 tsne_0.1-3
## [58] htmlwidgets_1.3 httr_1.4.0 FNN_1.1.3
## [61] gplots_3.0.1.1 RColorBrewer_1.1-2 shinyAce_0.3.3
## [64] fpc_2.1-11.1 acepack_1.4.1 modeltools_0.2-22
## [67] ica_1.0-2 pkgconfig_2.0.2 flexmix_2.3-14
## [70] nnet_7.3-12 labeling_0.3 tidyselect_0.2.5
## [73] rlang_0.3.1 reshape2_1.4.3 later_0.8.0
## [76] cellranger_1.1.0 munsell_0.5.0 tools_3.5.0
## [79] cli_1.0.1 generics_0.0.2 broom_0.5.1
## [82] ggridges_0.5.1 evaluate_0.13 shinyBS_0.61
## [85] yaml_2.2.0 npsurv_0.4-0 knitr_1.21
## [88] bit64_0.9-7 fitdistrplus_1.0-14 robustbase_0.93-3
## [91] caTools_1.17.1.1 randomForest_4.6-14 RANN_2.6.1
## [94] pbapply_1.4-0 nlme_3.1-137 mime_0.6
## [97] slam_0.1-44 xml2_1.2.0 hdf5r_1.0.0
## [100] compiler_3.5.0 rstudioapi_0.9.0 png_0.1-7
## [103] lsei_1.2-0 stringi_1.3.1 highr_0.7
## [106] lattice_0.20-35 trimcluster_0.1-2.1 HSMMSingleCell_1.2.0
## [109] pillar_1.3.1 combinat_0.0-8 Rdpack_0.10-1
## [112] lmtest_0.9-36 data.table_1.12.0 bitops_1.0-6
## [115] gbRd_0.4-11 httpuv_1.5.1 R6_2.4.0
## [118] latticeExtra_0.6-28 promises_1.0.1 KernSmooth_2.23-15
## [121] gridExtra_2.3 codetools_0.2-15 MASS_7.3-51.1
## [124] gtools_3.8.1 assertthat_0.2.0 withr_2.1.2
## [127] qlcMatrix_0.9.7 diptest_0.75-7 doSNOW_1.0.16
## [130] hms_0.4.2 grid_3.5.0 rpart_4.1-13
## [133] class_7.3-14 rmarkdown_1.11 segmented_0.5-3.0
## [136] Rtsne_0.15 lubridate_1.7.4 shiny_1.2.0
## [139] base64enc_0.1-3